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- EMDB-1609: VP6-VP7 complex structure from VP7 recoated rotavirus DLP -

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Basic information

Entry
Database: EMDB / ID: 1609
TitleVP6-VP7 complex structure from VP7 recoated rotavirus DLP
Map dataT13 non-icosahedral local averaging
SampleVP7 recoated rotavirus DLP:
VP7 / VP6 / VP2
Keywordsrotavirus / capsid / VP7 / VP6 / VP2
Function / homologyRotavirus major capsid protein VP6 / Rotavirus VP2 protein / Glycoprotein VP7 / Viral capsid/haemagglutinin protein / Virus capsid protein, alpha-helical / Rotavirus VP2 / Glycoprotein VP7 / Rotavirus A/C, major capsid protein VP6 / host cell endoplasmic reticulum lumen / viral intermediate capsid ...Rotavirus major capsid protein VP6 / Rotavirus VP2 protein / Glycoprotein VP7 / Viral capsid/haemagglutinin protein / Virus capsid protein, alpha-helical / Rotavirus VP2 / Glycoprotein VP7 / Rotavirus A/C, major capsid protein VP6 / host cell endoplasmic reticulum lumen / viral intermediate capsid / T=13 icosahedral viral capsid / T=2 icosahedral viral capsid / viral inner capsid / viral outer capsid / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral nucleocapsid / viral envelope / structural molecule activity / RNA binding / metal ion binding / Inner capsid protein VP2 / Inner capsid protein VP2 / Intermediate capsid protein VP6 / Outer capsid glycoprotein VP7
Function and homology information
SourceBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / 4.2 Å resolution
AuthorsChen JZ / Settembre EC / Aoki ST / Zhang X / Bellamy AR / Dormitzer PR / Harrison SC / Grigorieff N
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2009
Title: Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM.
Authors: James Z Chen / Ethan C Settembre / Scott T Aoki / Xing Zhang / A Richard Bellamy / Philip R Dormitzer / Stephen C Harrison / Nikolaus Grigorieff
Validation ReportPDB-ID: 3gzt

SummaryFull report
PDB-ID: 3gzu

SummaryFull report
About validation report
DateDeposition: Mar 25, 2009 / Header (metadata) release: Apr 8, 2009 / Map release: May 18, 2009 / Last update: Mar 9, 2012

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Structure visualization

Movie
  • Colored surface
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_1609.map.gz (map file in CCP4 format, 3268 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
108 pix
1.23 Å/pix.
= 133.164 Å
88 pix
1.23 Å/pix.
= 108.504 Å
88 pix
1.23 Å/pix.
= 108.504 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.233 Å
Density
Contour Level:2 (by author), 2 (movie #1):
Minimum - Maximum-4.63558674 - 6.8486414
Average (Standard dev.)-1E-8 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions8888108
Origin000
Limit8787107
Spacing8888108
CellA: 108.504005 Å / B: 108.504005 Å / C: 133.164 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2331.2331.233
M x/y/z8888108
origin x/y/z0.0000.0000.000
length x/y/z108.504108.504133.164
α/β/γ90.00090.00090.000
start NX/NY/NZ-17-17-200
NX/NY/NZ123123401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS8888108
D min/max/mean-4.6366.849-0.000

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Supplemental data

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Sample components

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Entire VP7 recoated rotavirus DLP

EntireName: VP7 recoated rotavirus DLP / Number of components: 3 / Oligomeric State: icosahedral virus capsid
MassTheoretical: 60 MDa / Experimental: 60 MDa / Measured by: Sum of all components

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Component #1: protein, VP7

ProteinName: VP7 / a.k.a: VP7 / Oligomeric Details: Trimer / Number of Copies: 780 / Recombinant expression: No
MassTheoretical: 37.4 kDa / Experimental: 37.4 kDa
SourceSpecies: Bos taurus (cattle)

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Component #2: protein, VP6

ProteinName: VP6 / a.k.a: VP6 / Oligomeric Details: Trimer / Recombinant expression: No / Number of Copies: 780
MassTheoretical: 44.8 kDa / Experimental: 44.8 kDa
SourceSpecies: Bos taurus (cattle)

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Component #3: protein, VP2

ProteinName: VP2 / a.k.a: VP2 / Oligomeric Details: Dimer / Recombinant expression: No / Number of Copies: 120
MassTheoretical: 94 kDa / Experimental: 94 kDa
SourceSpecies: Bos taurus (cattle)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 5 mg/ml / Buffer solution: 20mM Tris-HCl, 50mM NaCl, 2mM CaCl2 / pH: 8
Support filmC-flat grid
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 90 % / Method: Blot for 3 seconds before plunging / Details: Vitrification instrument: manual plunger

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30 / Date: Dec 1, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal), 58168 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 3500 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 90 K ( 90 - 90 K)
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 148 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 12 / OD range: 1.2

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 3780
Details: The particles were selected using SIGNATURE, the density map was reconstructed and refined using FREALIGN.
3D reconstructionAlgorithm: Projection matching / Software: FREALIGN / CTF correction: Individual particle / Resolution: 4.2 Å / Resolution method: FSC 0.143

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Atomic model buiding

Output model

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